Hi Gang,
In response to your suggestion, I updated my XCode, XCode Command Tools, and Fink. However, I'm still getting the R_io error...
In case it's helpful: After the XCode, XCode Command Tools and Fink updates, running the system_profiler SPDeveloperToolsDataType command at the terminal reveals the following:
~ % system_profiler SPDeveloperToolsDataType
Developer:
Developer Tools:
Version: 10.3 (10G8)
Location: /Applications/Xcode.app
Applications:
Xcode: 10.3 (14492.2)
Instruments: 10.2.1 (64492.2)
SDKs:
iOS:
12.4: (16G73)
iOS Simulator:
12.4: (16G73)
macOS:
10.14: (18G74)
tvOS:
12.4: (16M567)
tvOS Simulator:
12.4: (16M567)
watchOS:
5.3: (16U567)
watchOS Simulator:
5.3: (16U567)
Running afni_system_check.py is nearly the same as before with the same error, but updated fink version:
~ % afni_system_check.py -check_all
-------------------------------- general ---------------------------------
architecture: 64bit
system: Darwin
release: 18.7.0
version: Darwin Kernel Version 18.7.0: Tue Aug 20 16:57:14 PDT 2019; root:xnu-4903.271.2~2/RELEASE_X86_64
distribution: 10.14.6 x86_64
number of CPUs: 8
apparent login shell: csh
shell RC file: .cshrc (exists)
--------------------- AFNI and related program tests ---------------------
which afni : /Users/laurenlebois/abin/afni
afni version : Precompiled binary macos_10.12_local: Mar 30 2020
: AFNI_20.0.24 'Galba'
AFNI_version.txt : AFNI_20.0.24, macos_10.12_local, Mar 30 2020
which python : /sw/bin/python
python version : 2.7.11
which R : /usr/local/bin/R
R version : R version 3.5.3 (2019-03-11) -- "Great Truth"
which tcsh : /bin/tcsh
instances of various programs found in PATH:
afni : 1 (/Users/laurenlebois/abin/afni)
R : 1 (/Library/Frameworks/R.framework/Versions/3.5/Resources/bin/R)
python : 2
/sw/bin/python2.7
/usr/bin/python
python2 : 0
python3 : 0
testing ability to start various programs...
afni : success
suma : success
3dSkullStrip : success
uber_subject.py : success
3dAllineate : success
3dRSFC : success
SurfMesh : success
3dClustSim : success
3dMVM : FAILURE
Error in dyn.load(ll) :
unable to load shared object '/Users/laurenlebois/abin/R_io.so':
dlopen(/Users/laurenlebois/abin/R_io.so, 6): Library not loaded: /sw/lib/libjpeg.9.dylib
Referenced from: /Users/laurenlebois/abin/R_io.so
Reason: Incompatible library version: R_io.so requires version 12.0.0 or later, but libjpeg.9.dylib provides version 11.0.0
Calls: source ... withVisible -> eval -> eval -> set_R_io -> dyn.load
Execution halted
checking for R packages...
rPkgsInstall -pkgs ALL -check : success
R RHOME : /Library/Frameworks/R.framework/Resources
checking for $HOME files...
.afnirc : found
.sumarc : found
.afni/help/all_progs.COMP : found
------------------------------ python libs -------------------------------
++ module loaded: PyQt4
module file : /usr/local/lib/python2.7/site-packages/PyQt4/__init__.pyc
** failed to load module matplotlib.pyplot
-- matplotlib.pyplot is not required, but is desirable
-- python binaries under /sw/bin:
/sw/bin/python (sym link to /sw/bin/python2.7)
/sw/bin/python2.7
-------------------------------- env vars --------------------------------
PATH = /opt/local/bin:/opt/local/sbin:/usr/local/fsl/bin:/opt/local/bin:/opt/local/sbin:/sw/bin:/sw/sbin:/Applications/freesurfer/bin:/Applications/freesurfer/fsfast/bin:/Applications/freesurfer/tktools:/usr/local/fsl/bin:/Applications/freesurfer/mni/bin:/sw/bin:/opt/local/bin:/opt/local/sbin:/usr/local/fsl/bin:/opt/local/bin:/opt/local/sbin:/Applications/freesurfer/bin:/Applications/freesurfer/fsfast/bin:/Applications/freesurfer/tktools:/usr/local/fsl/bin:/Applications/freesurfer/mni/bin:/sw/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Users/laurenlebois/abin:/Users/laurenlebois/Programs_Misc:/Users/laurenlebois/scripts:/opt/local/bin:opt/local/sbin:/bin:/Applications/gedit.app/Contents/MacOS:/opt/local/bin:/opt/local/sbin:/Users/laurenlebois/osx:/usr/local/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Users/laurenlebois/abin:/Applications/mricron:/Applications/mricron/dcm2niix:/Applications/freesurfer:/Applications/R:/opt/X11/bin:/Users/laurenlebois/abin:/Users/laurenlebois/Programs_Misc:/Users/laurenlebois/scripts:/opt/local/bin:opt/local/sbin:/bin:/Applications/gedit.app/Contents/MacOS:/opt/local/bin:/opt/local/sbin:/Users/laurenlebois/osx:/usr/local/bin:/opt/local/bin:/opt/local/sbin:/usr/local/fsl/bin:/opt/local/bin:/opt/local/sbin:/Applications/freesurfer/bin:/Applications/freesurfer/fsfast/bin:/Applications/freesurfer/tktools:/usr/local/fsl/bin:/Applications/freesurfer/mni/bin:/sw/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Users/laurenlebois/abin:/Users/laurenlebois/Programs_Misc:/Users/laurenlebois/scripts:/opt/local/bin:opt/local/sbin:/bin:/Applications/gedit.app/Contents/MacOS:/opt/local/bin:/opt/local/sbin:/Users/laurenlebois/osx:/usr/local/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Users/laurenlebois/abin:/Applications/mricron:/Applications/mricron/dcm2niix:/Applications/freesurfer:/Applications/R:/opt/X11/bin:/Users/laurenlebois/abin:/Applications/mricron:/Applications/mricron/dcm2niix:/Applications/freesurfer:/Applications/R
PYTHONPATH = /usr/local/lib/python2.7/site-packages
R_LIBS =
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH (sub-shell) = /opt/X11/lib/flat_namespace
DYLD_FALLBACK_LIBRARY_PATH (sub-shell) = FSL_DIR /usr/local/fsl
------------------------------ data checks -------------------------------
data dir : found AFNI_data6 under $HOME
top history: ... [rickr]: updated FT_white.nii w/out 16 (brain stem)
data dir : found AFNI_demos under $HOME
top history: ... [pault]: remove rank from FATCAT_DEMO, FAT_MVM_DEMO
data dir : found suma_demo under $HOME
top history: .../SUMA_data/Build_tmp on Wed Aug 20 10:04:23 EDT 2014
data dir : missing afni_handouts
atlas : found TT_N27+tlrc under .
------------------------------ OS specific -------------------------------
XQuartz version : 2.7.11
which fink : /sw/bin/fink
fink version : Package manager version: 0.45.1
which brew : /usr/local/bin/brew
brew version : Homebrew 2.2.11
which port : /opt/local/bin/port
port version : Error: Current platform "darwin 18" does not match expected platform "darwin 14"
++ found 'brew' at /usr/local/bin/brew
++ found 1 dylib files under '/opt/X11/lib/flat_namespace'
-- found 'libXt' dylib files:
/opt/X11/lib/flat_namespace/libXt.6.dylib
-- recent OS X, cheating to check DYLD_LIBRARY_PATH in cur shell 'csh'...
++ found evar DYLD_LIBRARY_PATH = /opt/X11/lib/flat_namespace
========================= summary, please fix: =========================
* AFNI programs show FAILURE
* insufficient data for AFNI bootcamp
Any advice greatly appreciated.
Best,
Lauren
